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- PDB-1ry7: Crystal Structure of the 3 Ig form of FGFR3c in complex with FGF1 -

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Basic information

Entry
Database: PDB / ID: 1ry7
TitleCrystal Structure of the 3 Ig form of FGFR3c in complex with FGF1
Components
  • Fibroblast growth factor receptor 3
  • Heparin-binding growth factor 1
KeywordsGROWTH FACTOR/GROWTH FACTOR RECEPTOR / FGF-FGFR Complex / beta trefoil / Ig domain / GROWTH FACTOR-GROWTH FACTOR RECEPTOR COMPLEX
Function / homology
Function and homology information


t(4;14) translocations of FGFR3 / negative regulation of developmental growth / fibroblast growth factor receptor apoptotic signaling pathway / Signaling by FGFR3 fusions in cancer / bone maturation / chondrocyte proliferation / endochondral bone growth / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis ...t(4;14) translocations of FGFR3 / negative regulation of developmental growth / fibroblast growth factor receptor apoptotic signaling pathway / Signaling by FGFR3 fusions in cancer / bone maturation / chondrocyte proliferation / endochondral bone growth / mesonephric epithelium development / branch elongation involved in ureteric bud branching / regulation of endothelial tube morphogenesis / FGFR3b ligand binding and activation / regulation of endothelial cell chemotaxis to fibroblast growth factor / positive regulation of phospholipase activity / Signaling by activated point mutants of FGFR3 / FGFR3c ligand binding and activation / Phospholipase C-mediated cascade; FGFR3 / FGFR2b ligand binding and activation / fibroblast growth factor receptor binding / FGFR2c ligand binding and activation / Activated point mutants of FGFR2 / Phospholipase C-mediated cascade; FGFR2 / FGFR4 ligand binding and activation / endochondral ossification / FGFR1b ligand binding and activation / Phospholipase C-mediated cascade; FGFR4 / Signaling by activated point mutants of FGFR1 / fibroblast growth factor receptor activity / FGFR1c ligand binding and activation / organ induction / Downstream signaling of activated FGFR1 / Phospholipase C-mediated cascade: FGFR1 / bone morphogenesis / S100 protein binding / positive regulation of tyrosine phosphorylation of STAT protein / Signaling by FGFR2 IIIa TM / PI-3K cascade:FGFR3 / PI-3K cascade:FGFR2 / PI-3K cascade:FGFR4 / PI-3K cascade:FGFR1 / positive regulation of sprouting angiogenesis / bone mineralization / fibroblast growth factor binding / positive regulation of MAP kinase activity / positive regulation of intracellular signal transduction / positive regulation of cell division / PI3K Cascade / anatomical structure morphogenesis / fibroblast growth factor receptor signaling pathway / activation of protein kinase B activity / cell surface receptor signaling pathway via JAK-STAT / chondrocyte differentiation / SHC-mediated cascade:FGFR3 / SHC-mediated cascade:FGFR2 / SHC-mediated cascade:FGFR4 / SHC-mediated cascade:FGFR1 / transport vesicle / FRS-mediated FGFR3 signaling / FRS-mediated FGFR2 signaling / FRS-mediated FGFR4 signaling / FRS-mediated FGFR1 signaling / Signaling by FGFR3 in disease / neurogenesis / Signaling by FGFR2 in disease / Signaling by FGFR1 in disease / extracellular matrix / positive regulation of endothelial cell migration / lung development / regulation of cell migration / epithelial cell proliferation / positive regulation of epithelial cell proliferation / skeletal system development / Negative regulation of FGFR3 signaling / growth factor activity / Negative regulation of FGFR2 signaling / Negative regulation of FGFR4 signaling / Negative regulation of FGFR1 signaling / wound healing / positive regulation of cholesterol biosynthetic process / receptor protein-tyrosine kinase / integrin binding / positive regulation of angiogenesis / Constitutive Signaling by Aberrant PI3K in Cancer / cell-cell signaling / PIP3 activates AKT signaling / MAPK cascade / heparin binding / cellular response to heat / PI5P, PP2A and IER3 Regulate PI3K/AKT Signaling / RAF/MAP kinase cascade / protein tyrosine kinase activity / angiogenesis / cell cortex / positive regulation of ERK1 and ERK2 cascade / positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction / receptor complex / positive regulation of MAPK cascade / positive regulation of cell migration / positive regulation of cell population proliferation / cell surface / endoplasmic reticulum
Similarity search - Function
Fibroblast growth factor receptor 3 transmembrane domain / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil ...Fibroblast growth factor receptor 3 transmembrane domain / HBGF/FGF family signature. / Fibroblast growth factor family / Fibroblast growth factor / Acidic and basic fibroblast growth factor family. / Fibroblast growth factor receptor family / Cytokine IL1/FGF / Trefoil (Acidic Fibroblast Growth Factor, subunit A) - #50 / Trefoil (Acidic Fibroblast Growth Factor, subunit A) / Trefoil / Immunoglobulin domain / Immunoglobulin I-set / Immunoglobulin I-set domain / : / Immunoglobulin subtype 2 / Immunoglobulin C-2 Type / Tyrosine-protein kinase, catalytic domain / Tyrosine kinase, catalytic domain / Tyrosine protein kinases specific active-site signature. / Immunoglobulin subtype / Immunoglobulin / Tyrosine-protein kinase, active site / Serine-threonine/tyrosine-protein kinase, catalytic domain / Protein tyrosine and serine/threonine kinase / Ig-like domain profile. / Immunoglobulin-like domain / Immunoglobulin-like domain superfamily / Protein kinase, ATP binding site / Protein kinases ATP-binding region signature. / Immunoglobulin-like fold / Protein kinase domain profile. / Protein kinase domain / Immunoglobulins / Protein kinase-like domain superfamily / Immunoglobulin-like / Sandwich / Mainly Beta
Similarity search - Domain/homology
Fibroblast growth factor 1 / Fibroblast growth factor receptor 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3.2 Å
AuthorsOlsen, S.K. / Ibrahimi, O.A. / Raucci, A. / Zhang, F. / Eliseenkova, A.V. / Yayon, A. / Basilico, C. / Linhardt, R.J. / Schlessinger, J. / Mohammadi, M.
CitationJournal: Proc.Natl.Acad.Sci.Usa / Year: 2004
Title: Insights into the molecular basis for fibroblast growth factor receptor autoinhibition and ligand-binding promiscuity.
Authors: Olsen, S.K. / Ibrahimi, O.A. / Raucci, A. / Zhang, F. / Eliseenkova, A.V. / Yayon, A. / Basilico, C. / Linhardt, R.J. / Schlessinger, J. / Mohammadi, M.
History
DepositionDec 19, 2003Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 10, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 29, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Aug 23, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Heparin-binding growth factor 1
B: Fibroblast growth factor receptor 3


Theoretical massNumber of molelcules
Total (without water)53,7772
Polymers53,7772
Non-polymers00
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2980 Å2
ΔGint-16 kcal/mol
Surface area18310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.223, 64.748, 99.932
Angle α, β, γ (deg.)90.00, 94.67, 90.00
Int Tables number5
Cell settingmonoclinic
Space group name H-MC121

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Components

#1: Protein Heparin-binding growth factor 1 / HBGF-1 / Acidic fibroblast growth factor / AFGF / Beta-endothelial cell growth factor / ECGF-beta


Mass: 17482.697 Da / Num. of mol.: 1 / Fragment: FGF1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGF1 / Production host: Escherichia coli (E. coli) / References: UniProt: P05230
#2: Protein Fibroblast growth factor receptor 3 / FGFR-3 / tyrosine kinase JTK4


Mass: 36294.434 Da / Num. of mol.: 1 / Fragment: FGFR-3c
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: FGFR3c / Production host: Escherichia coli (E. coli) / References: UniProt: P22607
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71.4 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: Peg 4000, glycerol, MPD, cadmium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
116 %PEG40001reservoir
20.2 Mammonium sulfate1reservoir
35 %glycerol1reservoir
45 %MPD1reservoir
525000 nM1reservoirCdCl2
625 mMHEPES1droppH7.5
7150 mM1dropNaCl
814 mg/mlprotein1drop

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 1.277
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jul 3, 2003
RadiationMonochromator: Kohzu Double Crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.277 Å / Relative weight: 1
ReflectionResolution: 3.2→30 Å / Num. all: 11404 / Num. obs: 11404 / % possible obs: 98.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.68 % / Rsym value: 0.068 / Net I/σ(I): 13.8
Reflection shellResolution: 3.2→3.31 Å / Rsym value: 0.303 / % possible all: 95.5
Reflection
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 30 Å / Num. measured all: 41929 / Rmerge(I) obs: 0.068
Reflection shell
*PLUS
Highest resolution: 3.2 Å / % possible obs: 95.5 % / Rmerge(I) obs: 0.303

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Processing

Software
NameClassification
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: FGF1-FGFR1c complex (pdb id code 1EVT)

1evt


Resolution: 3.2→25 Å / Data cutoff high rms absF: 0 / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.341 1085 10.3 %random
Rwork0.277 ---
all0.2771 10502 --
obs0.2771 10502 --
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--15.849 Å20 Å243.158 Å2
2--25.513 Å20 Å2
3----9.664 Å2
Refinement stepCycle: LAST / Resolution: 3.2→25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2766 0 0 0 2766
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_mcbond_it2.0341.5
X-RAY DIFFRACTIONc_scbond_it2.6122
X-RAY DIFFRACTIONc_mcangle_it3.4642
X-RAY DIFFRACTIONc_scangle_it4.1552.5
Refinement
*PLUS
Highest resolution: 3.2 Å / Lowest resolution: 25 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS

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